This script is used to generate a bare-bones Nowcast report, where the modelled data generated in main_script_webversion.r is visualized using various techniques. Edit and stylize this report to suit your needs.

Below will list the modelled variants and their assigned supergroups only if the “WebteamX” model is specified (blank if not).

Trend plot

Each point represent the actual weekly proportions, while the curves and 95% prediction interval bands are estimated by the NML Nowcast model using the multinomial logistic regression approach. Variants are distinguished by colors. The dashed vertical line indicates the final day of the modelling period. Fitted curves to the right of the vertical line represent the forecasted projections.

The interactive plot presented below allows for the isolation of a chosen variant’s display through a double-click or the toggling of its display with a single click.

Stacked barplot

This visualization consists of two plots depicting the “Actual” and “Nowcast” proportions of Pango lineages within a given reporting epiweek. The upper plot, labeled “Actual,” is constructed based on existing counts extracted from genomic surveillance. The lower plot, labeled “Nowcast” showcases proportions estimated by the NML Nowcast model, which employs a multinomial logistic regression approach. A grey rectangle positioned at the top of the trailing weeks serves as an indicator of a period during which data may be incomplete.

The interactive plot presented below allows for the isolation of a chosen variant’s display through a double-click or the toggling of its display with a single click.

Pivot table

The pivot table below allows users to perform a range of functions on the modelled data to provide further insights. The default table provides predicted proportions for each variant (row) in each epiweek (column). This allows users to get the total proportion for a group of selected variants. To view the actual proportion, users can select “Actual Proportion (%)” in the dropdown menu. Users can also specify other mathematical functions on the data instead of “Sum”. Plots can be generated by changing the dropdown menu set with “Table” as the default. The user can also filter for specific variants and epiweeks by using the dropdown menu associated with either variable.

Coefficient plot

Each modeled variant is depicted as a point and distinguished by colors. The x-axis shows the corresponding proportion estimates for the final forecasted week, and the y-axis represents the daily selection coefficients relative to the reference group. The 95% prediction and confidence intervals of the proportion estimates and coefficients are illustrated through horizontal and vertical lines extending from the points, respectively.

Coefficient table

Below are the coefficient and intercepts for each modelled variant using the multinomial logistic regression model.

Logit plots

The logit plot of each modelled variant group with respect to the selected reference group.

Legal
Copyright Government of Canada 2023

Written by: National Microbiology Laboratory, Public Health Agency of Canada

Licensed under the Apache License, Version 2.0 (the “License”); you may not use this work except in compliance with the License. You may obtain a copy of the License at:

http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.